I swapped them around a bit and it seems to work now. Will post again if i run into further difficulties.
Apparently the winchester can handle 2x double sided and 2x single sided ram, which is what i now have.
To Clear things up for others that might have a problem like this:
Windows would not boot with 4 sticks of 512mb RAM
Rearranged RAM so the two new sticks were in slots 1+2 and the two old sticks were in slots 3+4
However, although windows booted fine, the ram was slowed to 100mhz as opposed to 200mhz and cas latency was 2.5.
I manually forced the ram to work at 200mhz and changed latency to 3 (i have been living with 1gb of cas3 and it has worked fine for 2 years).
Result - Winchester 3000 with 4x512mb of RAM running at DDR400 speeds.
Hope this helps someone in the future, it is very annoying when something doesn't work straight away, but with PCs i guess you just have to work the problem.
80gb + 250gb WD HDDs
X-FI Xtreme Music